Medhat Ibrahim

Analysis of the structure and vibrational spectra of glucose and fructose

Molecular modelling using semiempirical methods AM1, PM3, PM5 and, MINDO as well as the Density Functional Theory method BLYP/DZVP respectively were used to calculate the struc- ture and vibrational spectra of d-glucose and d-fructose in their open chain, α -anomer and β-anomer monohydrate forms. The calculated data show that both molecules are not linear; ground state and the number for the point-group C is equal to 1. Generally, the results indicate that there are similarities in bond lengths and vibrational modes of both molecules. It is concluded that DFT could be used to study both the structural and vibrational spectra of glucose and fructose.

Removal of Cd(II) and Pb(II) from aqueous solution using dried water hyacinth as a biosorbent

Possible usages of dried water hyacinth as biosorbent for metal ions were investigated. A model describing the plant is presented on density functional theory DFT and verified experimentally with FTIR. The model shows that water hyacinth is a mixture of cellulose and lignin. Dried shoot and root were found as good sorbent for Cd(II) and Pb(II) at optimum dosage of 5.0 g/l and pH 5.0; equilibrium time was attained within 30-60 min. The removal using root and shoot were nearly equal and reached more than 75% for Cd and more than 90% for Pb. Finally the second-order kinetics was the applicable model. Hydrogen bonds of reactive functional groups like COOH play the key role in the removal process.

Molecular Spectroscopic Study of River Nile Sediment in the Greater Cairo Region

The greater Cairo region is the most populated area in Egypt. The aquatic environment of the Nile River in this area is being affected by industrial activities. The study of the molecular structure of sediment may provide a good trace for such changes. Both Fourier transform infrared spectroscopy (FT-IR) and density functional theory (DFT) were used to study the effect of industrial waste disposal south of Cairo on the molecular structure of Nile River sediment. Four seasonal samples were collected from six sites covering 75 km along the Nile River. Grain sizes of 200 μm, 125 μm, 65 μm, and 32 μm, respectively, were examined. The results indicate that hydrated aluminum hydroxide controls the distribution of organic matter in the different grain sizes. Furthermore, the hydration of phenol may take place in grain sizes lower than 200 μm, which is indicated by the OH stretching at 3550 cm−1 and verified by the obtained model. The formation of metal carboxylate bonds at 1638 cm−1 (asymmetric) and 1382 cm−1 (symmetric) indicate the possible interaction between heavy metals and other organic structures, mainly humic substances.

Computational spectroscopic study of copper, cadmium, lead and zinc interactions in the environment

Molecular modelling has been used to investigate the interactions of various heavy metals, in order to understand and possibly to control the nature and behaviour of metals, especially in the aquatic environment. The interactions of copper, cadmium, lead and zinc with organic acids were studied using density functional theory (DFT) calculations. Carboxylic acid was used as a model molecule. The structure of each metal carboxylate was optimized and the vibrational spectrum calculated. The results indicate that there is a shift in the calculated vS(C=O) of metal carboxylates compared with that of carboxylic acid. It was also found that hexaaqua structures of both cadmium and zinc are stable whereas those of copper and lead are not. Furthermore, dipole moment calculations indicate that cadmium carboxylate dihydrate is more representative of cadmium interactions in the aquatic environment. Moreover, hexaaquo cadmium could further interact with surrounding molecules in the aquatic environment.

Molecular spectroscopic analysis of nano-chitosan blend as biosensor.

Chitosan/starch and chitosan/gelatin of different ratios were prepared following casting method. FTIR results indicate the formation of hydrogen bonding which dedicates the prepared blends for interaction with wide range of molecules specially those of NH₂ and COOH terminals. The results obtained with molecular modeling PM3 model are in agreement with spectroscopic data. As a result of increasing starch and gelatin in chitosan blends HOMO-LUMO energy slightly decreased while total dipole moment increased. UV-vis spectroscopy indicated the suitability of chitosan/starch blend as a glycine sensor. Further enhancement in the sensing performance of chitosan/starch blend was achieved by introducing 5 nm TiO₂ into the blend.

Structural and electronic properties of new fullerene derivatives and their possible application as HIV-1 protease inhibitors.

Density functional theory (DFT) calculations have been carried out at the hybrid Becke 3-Lee-Yang-Parr; B3LYP/3-21G** level of theory to study two series of hydroxy-chalca-acetic acid-(4-pyrrolidin-1-yl-phenyl) ester [C(60)-C(2)H(4)N-(4-XCOCH(2)OH)C(6)H(4)] and hydroxy-chalcoacetic acid-[2-(2-hydroxy-acetylchalcanyl)-4-pyrrolidin-1-yl-phenyl] ester[C(60)-C(2)H(4)N-(3,4-XCOCH(2)OH)C(6)H(4)]. The X atom is O, S or Se for the two series. The vibrational spectra, physical, chemical, thermodynamics and Quantitative Structure Activity Relationship (QSAR) properties of the studied molecules are calculated and discussed. We have evaluated these molecules as HIV-1 protease inhibitors based on the hydrogenation interaction between the hydroxymethylcarbonyl (HMC) groups and the two aspartic acid of the HIV-1 protease active site. Results show that some of the investigated fullerene-based derivatives can be considered promising as HIV-1 protease inhibitors.

Molecular spectroscopic study for suggested mechanism of chrome tanned leather.

Collagen represents the structural protein of the extracellular matrix, which gives strength of hides and/or skin under tanning process. Chrome tan is the most important tanning agent all over the world. The methods for production of leather evolved over several centuries as art and engineering with little understanding of the underlying science. The present work is devoted to suggest the most probable mechanistic action of chrome tan on hide proteins. First the affect of Cr upon hide protein is indicated by the studied mechanical properties. Then the spectroscopic characterization of the hide protein as well as chrome tanned leather was carried out with Horizontal Attenuated Total Reflection (HATR) FT-IR. The obtained results indicate how the chromium can attached with the active sites of collagen. Molecular modeling confirms that chromium can react with amino as well as carboxylate groups. Four schemes were obtained to describe the possible interactions of chrome tan with hide proteins.

Distribution and bacterial bioavailability of selected metals in sediments of Ismailia Canal, Egypt

The spatial and temporal variability in concentrations of heavy metals, and the portion of the bioavailable metals for bacterial community of Ismailia Canal sediment were conducted. Furthermore, Fourier Transform Infrared Spectroscopy (FTIR) was employed to elucidate the molecular structure of the same sediment samples. Results indicate that Cu, Cr and Zn concentrations showed temporal variation (p<or=0.05). However Pb and Zn showed significant spatial variation (p<or=0.05). Also, the mean value of Pb and Zn in sediment is higher than the shale reference value. There were no temporal or spatial significant in the total viable bacterial count (TVBC) for all sites while Zn shows the highest affinity for bacterial uptake followed by Ni>Pb>Cu>Cr>Co. Also, the shift in the CO suggested that hydrated divalent metals are interacting with organic acids to form hexahydrated metals carboxylate. There were non-significant interactions between temporal and spatial variation for all the studied metals.

A novel structure for removal of pollutants from wastewater.

Dried water hyacinth was subjected to molecular modifications using quantum mechanical calculations. The model simulates the modified plant as 3 cellulose units, one lignin and some metal oxides namely CaO; FeO and Al(OH)3 are attached through O-Linkage. The model suggests the ability to remove inorganic pollutants from wastewater according to unique hydrogen bonding and high total dipole moment. Based on this model microspheres are synthesized in the laboratory from dried water hyacinth and chitosan following self-assembly method. FTIR spectrum of microspheres exhibits only the characteristic bands for raw materials which give strong evidence that the formed material is a composite. The analysis of SEM micrographes of microspheres showed that the fibers of water hyacinth are imbedded in the crosslinked chitosan matrix. Batch adsorption kinetic models revealed that the sorption of lead ions on microsphere was very fast and the equilibrium was rapidly attained within 30 min. and properly correlated with the second-order kinetic model. Different models of isotherm sorption were used to describe the Pb (II) adsorption onto microspheres. From Langmuir isotherm, the maximum adsorption capacity (q(max)) for Pb(II) was 312.5 mg/g, which is about 3 times higher than that of the crude hyacinth. The free energy (E) was 15.798 kJ/mol which shows that the sorption process is endothermic and the mechanism of reaction is an ion-exchange. Even after four cycles of adsorption-desorption, the adsorption capacity was maintained and the decline in efficiency was less than 10%.

Molecular spectroscopic analyses of gelatin

The molecular structure of gelatin was studied using Fourier transform infrared spectroscopy FTIR. The spectrum is subjected to deconvolution in order to elucidate the constituents of the molecular structure. B3LYP/6-31g** was used to study 13 amino acids then the scaled spectrum was compared to those of protein in order to describe the contribution of each amino acid into protein structure. A special interest was paid to the NH and C=O region. The reactivity of each amino acid was studied in terms of some important physical parameters like total dipole moment and HOMO/LUMO which describe the interaction of amino acid with their surrounding molecules. Results indicated that B3LYP/6-31g** model is a suitable and precise method for studying molecular structure of protein.